Over the last 2-3 weeks I spent a few hours here and there on validating the assembly sequence for mini CNC (http://www.contraptor.org/mini-cnc#assembly) and looking for spots in the alignment process that could use more documentation. One of such spots is the leadscrew alignment - I found that following a few simple rules and knowing how things might go wrong can really shorten the time it takes to get the leadscrew drive working. I will need to write it up in detail but here is the draft: http://www.contraptor.org/leadscrew-alignment

When I started Z-axis assembly, it became clear that the design wouldn't allow to easily perform the leadscrew alignment steps, so I ended up modifying Z-axis to accommodate that. By the way, one of the advantages of construction sets is that a new version of an assembled device doesn't require time/expense of making/buying modified parts, as the case may be with a traditional kit. I simply rearranged the existing parts - construction set is more like software in that sense.

Here is the new Z-axis:

The design allows to assemble and align each of the rails independently.

It also provides more Z axis travel - almost 3" (measured without Dremel). This may be useful for some of the attachments such as drill chuck.

The first tests went well, but when I replaced 6" flat plexi bracket on the rear of X stage with AL angle to enable grounding of the limit switches, I ran into um.. a runtime error when the X stage rear angle crashed into one of the stepper driver heatsinks with Z raised all the way up. I didn't really crash, X stage just kept going, getting more and more skewed as the top was blocked and the bottom continued to move.

So now I have to remove the entire X axis and (mostly) re-assemble and re-align it from scratch. However this means I can take care of another narrow assembly spot - securing X axis to Z stage. It's somewhat difficult with the wrench and using hex socket is almost impossible. There is no reason why the flat screw/nut at the end of the linear rail can't be removed/moved 1" inward - that way it won't interfere with the hex socket.

After finishing the mini-cnc build I eventually ended up umounting, and re-aligning every axis … And had to replace X and Y threaded rods because using them while not aligned actually bent the rod ( they were not perfectly straight before mounting, anyway ).
This should be put in RED somewhere at the top of the mini-cnc instructions : everything you don't do perfectly right, you will end up re-doing.
When first building I was under the illusion that everything I did not perfectly would be easy to fix once the machine would be finished : it's not.

Also, have you uploaded an updated sketch of the mini-cnc ?
I'll soon be making a sketch for a contrapteur version of it and may as well use the most recent version.

Still finalizing that mod - had to move the top crossbar 1" back after realizing that Dremel power cord would be jammed; this required changing some things around, but also helped to get the stepper driver heatsinks out of the way and improved Z travel. One unrelated issue that attracted attention is that X axis barely gets 6" of travel, and even that requires mounting X limit switches on the X stage's rear bracket. Otherwise X travel is more like 5.5".

Eg. adding 1" to the X axis support on each side, and putting the bearing mount there.
Did this only in sketchup, never tested IRL, so maybe it won't work, but I think it adds travel ( in mine the bearing holders are what stop the X stage ).
Also, it adds a second point for supporting the X motor's supporting angle :

I think I found a way to do it without rebuilding X axis :) The X travel is limited to 6" by Z axis sliding elements - see pic.

I could fix this relatively easily by moving X axis >1/4" away from Z stage (on the pic, to the left). Currently it's at 1/8" - there is a nut in between Z axis sliding element and X axis 12" angle. This should give me extra 1/4" of travel on each end.